Bioinformatics Data Skills

Errata for Bioinformatics Data Skills

Submit your own errata for this product.


The errata list is a list of errors and their corrections that were found after the product was released.

The following errata were submitted by our customers and have not yet been approved or disproved by the author or editor. They solely represent the opinion of the customer.


Color Key: Serious Technical Mistake Minor Technical Mistake Language or formatting error Typo Question Note Update



Version Location Description Submitted By Date Submitted
PDF Page xiv
Final paragraph

"By robust, I mean the your work is..." should read: "By robust, I mean that your work is..."

Anonymous  Apr 30, 2015 
PDF Page xvii
1st paragraph

"If you know a scripting language other than Python like Perl or Ruby, you’ll prepared to follow along most examples..." is presumably missing the word "be", although I think the use of the word "prepared" is a bit awkward here.

Anonymous  Apr 30, 2015 
PDF John Tukey Quote on Robust Research

It should be: The Technical Tools of Statistics (1964) John Tukey and not The Technical Skills of Statistics (1964) John Tukey.

Kedar Mhaswade  Dec 16, 2015 
PDF Page 8
Final paragraph

The final part of the penultimate sentence: "...four times it’s size?" should use "its" instead of "it's". (This is me being a pedant - sorry!)

Anonymous  Apr 30, 2015 
PDF Page 10
Recommendations for Robust Research 1st paragraph

"which is all the more reason to include apply the recommendations below" should be "which is all the more reason to apply the recommendations below"

Tyler Kent  Jan 26, 2016 
PDF Page 12
2nd paragraph of "Make Assertions" section

The final sentence should use "it's/it is crucial" instead of "its crucial".

Anonymous  Apr 30, 2015 
PDF Page 19
Final paragraph

"Others researchers..." should be "Other researchers...".

Anonymous  Apr 30, 2015 
PDF Page 20
1st paragraph

"harddrive" should be "hard drive". This appears twice in this paragraph.

Anonymous  Apr 30, 2015 
PDF Page 20
1st paragraph

In the final sentence: "...would later make your researcher nearly impossible...", it should say "research" instead of "researcher".

Anonymous  Apr 30, 2015 
PDF Page 21
Final paragraph

"In this cases..." should be reworded to either "In this case..." or "In these/such cases...".

Anonymous  Apr 30, 2015 
PDF Page 29
2nd paragraph

A through I, using a range like zmays[C-I]_R1.fastq should be C through I, using a range like zmays[C-I]_R1.fastq

Erwin Gaubitzer  Feb 10, 2021 
PDF Page 38
4th paragraph, quotation

Doug McIlory should be Doug McIlroy

Erwin Gaubitzer   Feb 10, 2021 
PDF Page 65
2nd complete pragraph

The line "Suppose a lab has a clever bioinformatician that writes a script for trims poor quality regions from reads" I think that "for trims" should read "that trims"

Chris Hamm  May 06, 2014 
PDF Page 66
Last full paragraph

The sentence "Working with Git working with these commits" Maybe should read "When working with Git we use these comments"

Chris Hamm  May 06, 2014 
Printed Page 139
3rd text paragraph under 'Formatting Tabular Data with column'

'Note that you should only use columnt -t to visualize...' -> should this be 'column -t' instead? I don't think columnt is a valid command

Sam Du  Oct 12, 2020 
PDF Page 214
Final paragraph

The variable "d" here should be "reps".

Anonymous  May 12, 2015 
PDF Page 231
last line of code... follow(qry, sbj)

The output of follow() is incorrect; it looks like the new sbj was not loaded into R. The correct answer is 2. I'm going to stop submitting typos and errors because they aren't getting fixed. I realize that this is a pre-release but it seems like O'Reilly is slacking in their editorial responsibilities. That is unfortunate, because there are a lot of typos.

Chris Hamm  Jul 20, 2014 
Printed Page 290
Code

This line is incorrect: sbj <- IRanges(start = c(2, 4, 18, 19), end = c(4, 5, 21, 24)), names = 1:4) It does not produce the anticipated answers shown later in the code (specifically, the results for follow(qry, sbj) are incorrect. As shown in Figure 9-16 on the next page, the author intended for this line to be: sbj <- IRanges(start = c(2, 4, 18, 19), end = c(4, 6, 21, 24)), names = 1:4) The 5 should be a 6 in the vector of end positions.

Anonymous  Dec 01, 2016 
Printed Page 293
bottom

In the printed book, the output for "xrle[xrle>3]" is: numeric-Rle of length 11 with 3 runs Lengths: 3 1 7 Values : 4 100 4 However, the correct output should be: > xrle[xrle>3] numeric-Rle of length 10 with 1 run Lengths: 10 Values : 4

Kai Tang  Aug 10, 2020 
Printed Page 316
2nd last paragraph

organisim() should be organism()

Anonymous  Dec 09, 2016 
PDF Page 362
United States

Text: "Querying information from a set gene models can become quite involved." s/from a set gene models/from a set of gene models/

Pat Gunn  Feb 14, 2015 
Printed Page 381
3rd paragraph

The original text is: "First, note that some positions such as 215,906,528 and 215,906,528 only contain the alternative allele (in the ALT column) <X>." Should this be: "First, note that some positions such as 215,906,528 and 215,906,529 only contain the alternative allele (in the ALT column) <X>." ?

Shun Liang  Nov 13, 2015 
Printed Page 456
3rd paragraph

"every table you create should have primary key column" should be "every table you create should have a primary key column".

Anonymous  May 05, 2021 
Printed Page 458
Last paragraph

"Unlike SQLite and PostgreSQL, which support multiple databases, each database in SQLite is a single file." First mention of SQLite should probably be MySQL.

Anonymous  May 05, 2021 
Printed Page 467
Last paragraph

"downloading and installing to new Python and R packages" should be "downloading and installing new Python and R packages"

Anonymous  May 05, 2021